Biology subjects

Semidey, M. E.

Publications and source records attributed to Semidey, M. E..

5 recordsLinked to original sources

bioRxiv2026

Site-Specific Entry Factors Define Cellular Susceptibility to SARS-CoV-2 in Human Tissues

SARS-CoV-2 primarily infects the respiratory epithelium through entry factors ACE2 and TMPRSS2. However, alternative viral entry receptors and/or modulators of viral entry factors expression may contribute to infection in respiratory as well as non-respiratory tissues, including the kidneys and colon. Using single-cell analyses, we identified novel candidates for spike-mediated viral entry in epithelial cells from diverse fresh human tissues exposed to a labeled spike-pseudotyped virus. Systematic viral tracking revealed tissue-specific membrane receptors that contribute to viral entry, functionally validated in human tissues and partially predicted by molecular modeling. We found ADAM17 and IL1R1, together with canonical molecules, to significantly facilitate viral entry in the lung parenchyma, while entry into the renal cortex was less dependable on canonical factors, but strongly modulated by JAK1/2 engagement. These findings uncover distinct viral entry mechanisms across tissues and suggest novel organ-specific therapeutic targets for patients at risk.

microbiology↗

bioRxiv2026

p21(CIP1/WAF1)-mediated partial senescence supports steroidogenesis and therapy resistance in primary prostate cancer cultures

BackgroundProgression of prostate cancer to castration-resistant disease is driven by early adaptive mechanisms that remain poorly defined. Increasing evidence suggests that senescence-associated programs and intratumoral steroidogenesis may contribute to therapeutic resistance, but their functional interplay in hormone-naive disease is unclear. MethodsHormone-naive primary prostate cancer cultures (hnPCs) were established from diagnostic biopsies and characterized for proliferation, therapeutic response, senescence markers, and steroidogenic gene expression. Functional relevance of CDKN1A was assessed by knockdown experiments. Public transcriptomic datasets from ETS fusion-negative, AR signaling inhibitor-naive metastatic castration-resistant prostate cancer (mCRPC) were interrogated for clinical validation. ResultshnPCs exhibited low proliferative capacity yet intrinsic resistance to androgen deprivation therapy and docetaxel. Most cultures displayed coordinated overexpression of CDKN1A/p21CIP1 together with steroidogenic enzymes, particularly AKR1C3, alongside p16INK4a expression and SA-{beta}-galactosidase activity, consistent with a partial senescence-like state. CDKN1A depletion selectively reduced AKR1C3 expression and increased proliferation in a subset of cultures, indicating that p21 maintains specific senescence-associated features while permitting adaptive plasticity. Analysis of ETS fusion-negative, ARSI-naive mCRPC tumors revealed positive correlations between CDKN1A and steroidogenic genes, supporting the translational relevance of this program. ConclusionsThese findings identify a previously underrecognized CDKN1A-associated partial senescence program that supports steroidogenic reprogramming, survival, and early therapeutic resistance in aggressive prostate cancer. This adaptive state may predispose tumors to progression toward castration resistance and represents a potential biomarker and therapeutic vulnerability in high-risk, ETS-negative disease.

cancer biology↗

bioRxiv2024

Evaluation of homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional tissue-based immunofluorescence assays

PurposeMetastatic prostate cancer (mPC) is enriched for homologous recombination repair (HRR) gene alterations; these biomarkers have prognostic and predictive value. Next-generation sequencing (NGS) allows for patient stratification based on these biomarkers, but widespread clinical implementation is still limited. Moreover, not all mutations in HRR genes result in functional HRR loss in the tumor. We investigated the correlation between genomic and functional loss of HRR, using NGS and an optimized RAD51 immunofluorescence (RAD51-IF) assay in mPC clinical biopsies. Experimental designObservational study including patients with stage IV prostate cancer. Biopsies from either primary tumor or metastatic biopsies underwent NGS (targeted sequencing and/or whole-exome sequencing), and RAD51-IF. Clinical data was extracted from electronic patient records. Results219 biopsies from 187 patients were acquired, including primary (151/219) and metastatic (68/219) tumor biopsies collected either in the metastatic hormone- sensitive (169/219) or castration-resistant (50/219) setting. NGS (181 biopsies from 157 patients) showed frequent genomic alterations in TP53 (40%), AR (15%), PTEN (14%), MYC (10%), BRCA2 (9%), ATM (8%) and BRCA1 (2%). Tissue for RAD51 IF was available for 206 samples; of those, 140/206 (68%) were evaluable for RAD51- IF. Based on a previously defined threshold of 10% RAD51-positive cells, 21% samples had RAD51-low results compatible with HRR deficiency (HRD). Sample matched RAD51-IF and genomics data were obtained for 128 biopsies (117 patients): RAD51-IF had a high sensitivity (68%) and specificity (85%) to identify cases with BRCA1/2 alterations. Additionally, the RAD51-IF assay was able to identify restoration of HRR function in selected cases with BRCA2 reversion mutations or BRCA1 expression. ConclusionsRAD51-IF is feasible in routine clinical samples from mPC patients and associates strongly with clinically relevant HRR gene alterations.

cancer biology↗

bioRxiv2023

Renal Cl-/H+ antiporter ClC-5 regulates collagen production and release in Dent Disease models

Mutations in the Cl-/H+ antiporter ClC-5 cause Dents Disease 1 (DD1), a rare primary tubulopathy that eventually progresses to renal failure. In fact, even with normal kidney function, DD1 patients present renal tubulointerstitial fibrosis. However, the link between ClC-5 loss-of-function and renal fibrosis remains unclear. Here, we have shown that DD1 mice models lacking ClC-5 present higher renal collagen deposition and fibrosis. Accordingly, deletion of ClC-5 in human renal proximal tubule epithelial cells (CLCN5 KD) recapitulates this effect. We have demonstrated that CLCN5 KD causes an increase of collagen I (Col I) and IV (Col IV) intracellular levels by promoting their transcription through {beta}-catenin pathway and impairing their lysosomal-mediated degradation. In addition, CLCN5 KD cells release more Col I and IV at the extracellular space that form fibres with altered properties and resistance to removal compared to control cells. Altogether, we describe a new regulatory mechanism for collagens production and release by ClC-5, which is altered in DD1 and provides a better understanding of disease progression to renal fibrosis. SIGNIFICANCE STATEMENTRenal fibrosis is a common pathologic process occurring as consequence of chronic kidney injury and leading to renal dysfunction. Dents Disease is a rare renal pathology that progresses to chronic kidney disease and tubulointerstitial fibrosis. Interestingly, it is caused by mutations in a single gene called CLCN5, therefore it can help understanding the cellular mechanisms of renal fibrosis. Using cellular and mice models of the disease, we describe a mechanism linking CLCN5 function, cell differentiation and regulation of collagen levels, major component of extracellular matrix and important player for renal fibrosis development. In conclusion, our results provide a link between CLCN5 and altered collagen deposition, which could be relevant for other renal Fanconi syndrome related diseases also progressing to fibrosis.

cell biology↗

bioRxiv2021

Temporal and sex-dependent gene expression patterns in a renal ischemia-reperfusion injury and recovery pig model

Men are more prone to acute kidney injury (AKI) and chronic kidney disease (CKD), progressing to end-stage renal disease (ESRD) than women. Severity and capacity to regenerate after AKI are important determinants of CKD progression, and of patient morbidity and mortality in the hospital setting. To determine sex differences during injury and recovery we have generated a female and male renal ischemia/reperfusion injury (IRI) pig model, which represents a major cause of AKI. Although no differences were found in blood urea nitrogen (BUN) and serum creatinine (SCr) levels between both sexes, females exhibited higher mononuclear infiltrates at basal and recovery, while males showed more tubular damage at injury. Global transcriptomic analyses of kidney biopsies from our IRI pig model revealed a sexual dimorphism in the temporal regulation of genes and pathways relevant for kidney injury and repair, which was also detected in human samples. Enrichment analysis of gene sets revealed five temporal and four sexual patterns governing renal IRI and recovery. Overall, this study constitutes an extensive characterization of the time and sex differences occurring during renal IRI and recovery at gene expression level and offers a template of translational value for further study of sexual dimorphism in kidney diseases. AUTHOR SUMMARYKidneys correct functioning is essential for optimal body homeostasis, being their basic functions blood filtration and excretion of wastes and toxins. Inherited or acquired conditions can cause renal dysfunction requiring renal replacement therapy, which will affect patients life quality and survival. A major cause of kidney failure is the renal ischemia/reperfusion injury (IRI), which occurs in many clinical situations like kidney transplantation or aortic aneurysm surgery. Interestingly, men are more susceptible to IRI than women, being women more protected against kidney injury. However, the genetics regulating these sex differences in injury and renal repair remained unknown. Here, we provide a novel porcine model to study renal injury and recovery in both males and females. Using this model, we have identified the gene sets involved in renal injury and recovery processes. Moreover, global genetic analyses allowed us to discover the temporal and sex-dependent patterns that regulate those gene sets and, finally, kidney damage and repair. A relevant finding of our study is that males develop a feminized genetic profile during recovery, which may represent a survival mechanism to diminish the androgenic pro-damage effects on kidney cells. To sum up, our results provide novel sex-dependent targets to prevent renal injury and promote kidney recovery.

genomics↗